Thursday, 22 January 2015

In-program shot showing the processing of data when making a 3D point cloud and mesh of a
nodosaurid spike from the Isle of Wight, UK.

It's been a year and a few days since I started my vertebrate palaeontology PhD working on a specimen of Polacanthus from the Wessex Formation of the Wealden Sub-basin on the Isle of Wight. I feel some profound changes have taken place for me as a researcher and as a person; I had read about how all-consuming doing a PhD was but until I was actually doing the research I didn't understand how obsessive I'd become about out the science and about ankylosaurs and thyreophorans. To be able to work on an actual skeleton was a boyhood dream come true, and I'm pleased to say I feel the same wonder now as I did then.

This particular specimen of Polacanthus had been acquired by the University of Southampton a year or two previously from a private collector and was found on the south-west coast of the island in the mid 1990s. However, the fossil had had a turbulent past as various elements of specimen were collected by different collectors, and there was some dispute over ownership of the bones. In the end, the two sides couldn't reach agreement and the skeletal elements were never reunited.

In addition to the my original project plan it was decided a comprehensive description was necessary before taking a look at the biomechanics. The first task was to assess how much of the specimen there is and what condition it was in, a task complicated by the fact the specimen is split between three institutions. The majority now resided at the National Oceanography Centre Southampton, the location of the Ocean and Earth Science department and home of the Soton VP group. Other parts of the skeleton are in the collections at Dinosaur Isle Museum at Sandown on the island itself and a water-worn ankylosaurid brain case thought to be associated with the specimen but recovered from the foreshore had ended up in the collections at The Sedgwick Museum in Cambridge.

On top of this, the skeleton is various states of preparation. As mentioned, the brain case was water-worn and had been sectioned along the sagittal plane to reveal the interior. The DI elements have been fully prepped and are in excellent condition. The Soton elements are in need of preparation and although some bones have been glued back together there is a fair amount or re-positioning and cleaning of matrix still to be done. On top of this the ilium is in several chunks and the sacral shield is in many small pieces, most around 1cm square and resembles a couple of boxes of roman tesserae; there is a considerable and laborious task ahead for someone . . .

I decided my first job was to record the bones as they were and I set out to record the whole skeleton in 3D using photogrammetry. This entailed taking multiple images of each bone on a turntable in increments of 10 or 20 degrees. The results were then processed in Agisoft Photoscan standard edition and 3D point clouds and meshes generated which meant I could begin to reconstruct the skeleton on the computer. It also meant that I could carry around detailed 3D models of all the bones both singly and reassembled on my iPad; I literally carry a dinosaur in my bag!

Next I visited a couple of collections to look at other Polacanthus specimens, most importantly the holotype at the NHM and the elements of the Soton specimen held at Dinosaur Isle. I recorded some of these bones using photogrammetry for comparison purposes, but most importantly I recorded the elements of the Soton specimen at Dinosaur Isle and this means the skeleton will be complete again, albeit in virtual space.

I have also been building a relationships with collectors on the island and beyond, although as many of these are friends already that hasn't been particularly difficult. We rely on the local collectors to bring significant finds to our attention and I love working with these people as they often have unparalleled knowledge of the stratigraphy and fossil assemblage of the outcrops that they patrol on a daily basis. I recently picked up a couple of specimens that I am currently working on that have been donated for study, and I hope to publish on these as soon as possible.

I attended the SVP in Berlin (with the most fantastic field trip ever) where I presented a poster on dinosaur tracks of the Isle of Wight and co-authored another along with Brent Breithaupt and lead author Neffra Matthews. The same team plus Martin Lockley and Jeremy Lockwood had co-authored my first paper as a first author Tracking Dinosaurs on the Isle of Wight: A review of tracks, sites and current research which was published in a special edition of the Biological Journal of the Linnean Sociey that was based on the Celebrating Dinosaur Isle: Jehol-Wealden meeting we had hosted at NOCS a year previously and I was also co-author on another two papers in that edition. A dinosaur trackers group is going to be established to enable collaboration between ichnologists worldwide and start some serious comparisons of ichnofacies of the early Cretaceous around the planet.

By the time my PhD panel meeting came around in December I was well into gathering data and beginning the virtual reconstruction of the skeleton. The meeting went better than I had hoped and I am aiming to upgrade in the early summer, which means I am proceeding faster than I originally envisaged and is great news. It was decided to refocus my PhD on the evolution and development of Polacanthus as the ongoing description and reconstruction revealed more about the specimen and this warranted investigation. This means a move away from the more comprehensive biomechanics work I originally intended to do, but that may we'll feature towards the concluding stages of the degree. It was also decided that I would do my PhD by publication, a decision I am very happy with as it means the research will get out there. Whilst this is going on another MRes student is looking at the histology of the specimen so this particular dinosaur is getting some serious attention at last.

3D mesh of the ulna of a juvenile nodosaur held in the collections at Dinosaur Isle, Sandown, Isle of Wight, UK.

I did have a hard decision to make with regards to methodology as the year came towards an end. I wasn't happy with some of the photogrammetry and decided to re-process everything I had already completed in order to get the best possible results. This has meant hand masking all the photographs I have taken as part of the re-processing workflow. Obviously such a major revision at this stage is not ideal but I decided that ensuring the data are as good as possible was essential, despite the fact this means hand-masking several thousands of photographs. This task is now complete and it's become obvious the decision was the correct one as the software has improved in the year I've been processing the photographic data and the results are far superior point clouds and meshes. There is still some photogrammetry to do but the majority of the work is done and I should have nearly the entire skeleton in 3D in a couple of months with the exception of the parts of the specimen that require extensive preparation or reconstruction; this will include the sacral shield and some of the caudal osteoderms. These can be reconstructed in the computer with a reasonable amount of confidence that any speculative reconstruction involved is based on solid data and comparisons. As an aside, this process has generated a serious amount of data, and I'll be considering the best way to archive this (it is backed up several times a day).

There are other issues of course, not least of which is money. It's not easy to discuss this subject without sounding like a whiner, but here goes. Being self-funded means I cannot afford to travel as much as I would like to, and I have to work on basic or old versions of software that a grant might otherwise pay for. Being a couple of hundred miles from the university has it's problems too, and although I am in constant contact with my supervisor via the phone and Skype it can feel a bit isolated. Luckily the Soton VP group are a superb bunch of people and I keep in contact over social media and via email. I get down to NOCS as often as possible but lack of funds imposes constraints, and that's a a fact of life. I'll be looking onto the various grants available in order to fund software purchases and travel.

One of the major concerns at from the outset was how being a researcher would fit with work. Being self-employed it was a no-brainer that work had to come first and research would have to fit around it. In practice this has worked well so far, and the flexibility I built into my PhD means I can work as usual and still get time to pursue my degree. Also the two activities feed back into each other, for example I'm able to understand the science that's being communicated in much of my work and find it easier to understand context and some of the technical aspects of my end clients research. Of course the creation of 3D graphics and models in my day job has proved invaluable in my research, and I'm still building this skill set even after 28ish years of working in the industry.

What we have to suffer for our science. Me having a terrible time on the SVP field trip to German lagerstätten last year.

Finally, I am really enjoying doing my PhD. It's proved to be quite challenging (I don't have an academic background), often a little daunting but never less than utterly fascinating and very rewarding and as I mentioned at the beginning it's become a real obsession. I've received excellent support from my supervisors, fellow students and RA's at Soton, friends at home and on the island as well as my family, especially my wife and parents.

This year sees the SVPCA being held in Southampton so I hope to see you there. The logo (designed and drawn by yours truly) features Polacanthus of course!

Monday, 24 November 2014

I thought I'd upload an image of the poster I presented at the SVP 2014 in Berlin earlier this month. The poster features some of the research discussed in a paper that was part of the special edition of The Biological Journal of the Linnean Society that was inspired by the successful Celebrating Dinosaur Island: Jehol-Wealden meeting held last year at the National Oceanography Centre, Southampton (see my write-up here). This paper, entitled Tracking Dinosaurs on the Isle of Wight: a review of tracks, sites, and current research (Pond et al, 2014) is a review of dinosaur ichnology on the Isle of Wight and looks at both tracks and sites. It came as a shock to realise many of these sites had never been written up and although they had been mentioned in a couple of book chapters Martill and Naish 2001 and Batten 2011) they had been pretty much ignored.

Also discussed in the paper was the presence of the thyreophoran ichnotaxa Tetrapodosaurus and Deltapodus, the latter having been assigned in a poster by Belvedere et al (2012) and which is interpreted as a having been made by a stegosaur. As Tetrapodosaurus is considered as having been made by an ankylosaurian track maker it seems possible there was more going on with thyreophorans in the Wessex Sub-Basin than was previously thought . . .

This paper was very much a team effort and big thanks to my co-authors Neffra Matthews, Brent Breithaupt, Martin Lockley and Jeremy Lockwood. I co-authored a couple of other papers with Martin, Jeremy and Lida Xing and all can be had from the link to the BJLS above (Unfortunately the papers are behind a paywall but if you want a copy of any of them then drop me a line and I'll send one on).

Friday, 29 August 2014

Indet. ornithopod caudal vertebra recorded using photogrammetry.
480,342 polygons, with and without texture.

Here’s a prediction: 3D meshes of dinosaur bones and ichnites will become the main method of interaction with specimens for many palaeontologists within a decade. While not a panacea for all the issues that access to specimens raises for workers, this trend might go some way to mitigating some of the more persistent problems associated with the process. This prediction might come across as either a little obvious or a rather hubristic depending on your current engagement with virtual specimens and either view might be correct, but here’s why I think it will happen.

As the technology for recording, creating, distributing and working with 3D models becomes ever more widely used it’s becoming apparent that the usefulness of 3D specimen data is far more than originally envisaged. The advent of 3D printing and the ubiquity of 3D content on the internet means that meshes provide robust, testable data that is can used in a variety of ways. Biomechanics, finite element analysis and morphometrics are already well-established uses for 3D data as are comparative and descriptive purposes, reconstruction and illustration. By returning data to the physical world by 3D printing, specimens can be shared without ever having to leave the collections they are accessioned to. It’s now possible to carry and entire dinosaur skeleton on an iPad, each bone viewable at any time. Physical interaction with specimens is at the core of what we do as palaeontologists and from the field to the lab we need to be able to work on actual fossils, and this will never change. However, this might not be the most pragmatic way for us to get to all the specimens we need and 3D meshes will provide a way of accessing specimens in the future.

Many ichnologists already do this and for them this is a no-brainer. Like many fossils, ichnites are often vulnerable to destruction and degradation, from collectors and erosion to specimens that need to remain in situ and are rightly afforded special protection so everyone can enjoy them. These can now be taken back to the lab (or pub) in as 3D data for study, recorded for research and posterity, a 3D snapshot in time. We can record how these resources change over the years, refer back to them countless times, and share them with each other easily.

For open access advocates, the rising popularity of 3D data for research should be a big deal. In an ideal world all described and figured specimens would be freely available for download at any time, by anybody. The ability to do this might have consequences for all palaeontologists, and the institutions specimens are housed in. One issue that continues to vex palaeontologists is the thorny issue of access to specimens in private and public collections. Whilst the argument that having first-hand access to a specimen is always best is irrefutable, practicalities dictate that it’s not always possible.

Vitally, free open-access to specimens for everyone (not just scientists) might have many more benefits. The commercial trade in fossils is a subject of huge concern to any palaeontologist. With the insidious tendrils of the free market feeling their way towards more and more specimens it is a real and present danger more that more data will be lost forever; the self-regulation of markets is a myth. However, if palaeontologists can gain access to private collections or collections about to be dumped on the market by institutions (as San Deigo Museum nearly did with their Sternberg collection) all is not lost. We can now record specimens held in these collections and archive the data in a way we’ve never been able to before; there’s a tremendous amount of data out there that never gets studied. Using high-quality 3D data will remove the need for direct access the fossils to a certain degree and allow specimens otherwise unavailable to science to be worked on. We all know of specimens that are languishing in collections and might disappear at any time, lost forever and never published up. By depositing 3D data in an open access repository there will be easily obtained testable data available for research.

This democratisation of data might have an important side effect if we could print off any fossil we wanted to. Fancy a .25 scale Tyrannosaurus rex skull on your mantlepiece? No problem, a specialist fabricators could print one off for a fraction of the price of the original. The kids want an ankylosaur spike for a school project? Download and print one off at the local high street print shop (or at home when the hardware becomes more affordable). This might be of help in pulling the rug from under a commercial fossil market that routinely prices important specimens out of the price range of virtually all public institutions; when they go, so so might the data they represent.

How could all this new data be curated? Firstly, there is now a real and present need for a cohesive set of standards to ensure the future viability of digital collections; file formats have a habit of becoming obsolete as technology races forward. Secondly, a single file format needs to be established as the standard for archiving and accessioning digital specimens. My own preference would be for Alias Wavefront’s .obj file standard for several reasons: it’s read by virtually every 3D program available, is robust, it can retain texture information in a separate jpeg file and includes the UV information relating to the texture.

Finally, an open-access online repository to hold this data, an idea that has been wafting around for a while (see this post by Peter Falkingham for example, on establishing a database of neoichnological digital specimes). This is the biggie, and the establishment of such a resource would raise some quite contentious issues. Uploading a mesh of a dinosaur footprint spotted on a beach or of a certain outcrop is one thing, but what would be the consequences of uploading the entire holotype of a dinosaur? Museum curators might get the howling fantods at the thought of their exclusive specimens being available for free online, potentially depriving them of revenue generated from visitors to their collections. After all, this data would be freely available and if someone had the urge to print an entire skeleton out and start their own museum they would be able to, without paying a penny. Would some sort of commercial licensing be necessary? Would institutions and individuals be able to veto the inclusion of specimens they hold in such a repository? Questions, questions . . .

At the end of the day, specimens held by public institutions are owned by the public and free, unfettered access to them by anyone is the ideal scenario. Of course it’s less than ideal to allow anyone in to have a gander at your one-of-a-kind ultra-delicate fossil, but by making an accurate 3D mesh of that fossil available for all then you won’t need to; just download and print one off! For scientists and the public alike, there’s great potential in this technology if only we can all agree at the outset of how we can curate and manage it.

Not a palaeontologist? Well, you could always share heritage items such as this 3D mesh of a2.5m recumbent stone from Arbor Low stone circle in the White Peak of Derbyshire, UK.Send it to anyone with an internet connection. You can't do that with the real thing.

Monday, 18 August 2014

The illustration from Lee's report of 1843 of a single osteoderm and surrounding ossicles.

The first sign that there was an armoured dinosaur present in the rocks of Wealden Sub-Basin of the Isle of Wight was when one John Edward Lee reported the existence of three fossils from the Hastings Beds of Sandown on the Isle of Wight way back in 1843. However, the Hastings Beds don’t outcrop on the island, so if they didn’t actually come from there where did they come from? Lee describes these fossils as ‘dermal plates’, and goes on to describe them at length in his paper. Only one is illustrated however, and this and the second plate were sent to Mr. Sowerby (presumably this is James De Calre Sowerby, a mineralogist and illustrator who co-founded the Royal Botanical Society and Gardens) in a hackney carriage along with drawings of the fossils destined for publication in the Annal of Natural History. The third was in poor condition and not deemed worthy of illustration and is still held in the Natural History Museum, London (BMNH R643) according to Pereda-Suberbiola. The surviving illustration clearly shows a single large osteoderm surrounded by smaller ossicles, themselves set amongst more ossicles. This certainly looks like a section of Polacanthus sacral shield, but is it?

The holotype of Polacanthus was found by the remarkable Rev. Fox of Brixton (now Brighstone) on the Isle of Wight around 1865. Fox had found the shield intact but it crumbled as he excavated the specimen, and when J.W. Hulke finally got around to describing the fossil in 1881 the shield was still in numerous small bits. Five years passed and Hulke revisited Fox’s Polacanthus, the shield of which had been reconstructed piece-by-piece by the remarkable efforts of a Mr. Hall and Mr. Barlow. This revealed the ornamented upper surface of the shield which Hulke describes in some detail, including the arrangement of larger keeled osteoderms amongst smaller ossicles, very similar to Lee’s specimen. Polacanthus is not the only nodosaurid (if Polacanthus is actually a nodosaurid, but that’s another story) with a sacral shield, and a comparison via the literature with sister taxa such as Mymroopelta and Gastiona reveal their sacral shields were similarly ornamented (see illustration below).

A selection of osteoderms and ossicle arrangements from various nodosaurids.
Lee's specimen is top right, the others are redrawn from various papers.

It’s likely that Lee’s specimens were the first remains of a Polacanthus sacral shield ever reported. As was mentioned earlier, the fossils probably didn’t come from the Hastings Beds as they aren’t present on the Isle of Wight; Pereda-Suberbiola suggests these remains are from the Wessex Formation at Brook Bay (Pereda-Suberbiola, 1994), although a part of the Wessex Formation is exposed in the cliff at Sandown and he doesn’t give his reasons for favouring this location. As for the fossils themselves, Lee was an astute observer and commented on the histology of the osteoderms, recognising the fibrous nature of the bones. He compared them with the scales of extant iguanas and crocodilians, and despite the fragmentary nature of the material found no reason to connect them with lizards or crocodiles.

The two ‘plates’ and drawings never made it to Sowerby. They were sent in a hackney carriage but never arrived and so joined the list of other dinosaur specimens lost to science. Had they had done, it’s entirely plausible that Polacanthus would have been named twenty years before it actually was.

References:

Hulke, J.W. 1881. Polacanthus foxii, a large undescribed dinosaur from the Wealden Formation in the Isle of Wight. Philosophical Transactions of the Royal Society of London, Vol. 172; 653-662.

Hulke, J. W. 1887. Supplemental note on Polacanthus foxii, describing the dorsal shield and some parts of the endoskeleton, imperfectly known in 1881. Philosophical Transactions of the Royal Society of London, Vol. 178: 169-72.

Lee, J.E. 1843. Notice of Saurian Dermal Plates from the Wealden of the Isle of Wight. Annals of Natural History. London. 11: 5-7.

Wednesday, 23 July 2014

If by some chance the human race manages to survive itself and thrive in the far future, it's likely we will one day explore the other planets in our solar system and perhaps beyond. Future exopalaeontologists and exoichnologists will have exciting jobs, looking for traces of past life on other planets. But could they actually recognise them in the field?

Neoichnology is the study and recording of modern traces to assist us in our understanding of the traces left by past life, and is an important part of an ichnologists work. The current standout work on neoichnology is Tony Martin's excellent Life Traces of the Georgia Coast, a book that is packed with insights into the process of trace making by the denizens of the barrier islands off the coast of the southern USA (Tony's excellent blog is here). For an example of neoichnological data gathering using photogrammetry see this previous post.

One technology that is very well suited to palaeontology and ichnology work in particular is photogrammetry. I've posted before on the subject and there is a discussion and primer here and here. One of the huge advantages of photogrammetry is you don't actually have to visit a site personally to obtain accurate data. For palaeontologists unable to get into the field this means we can still work on data collected by colleagues and, er, robots.

Robots? As it turns out, yes. Currently Mars has two operational NASA rovers on it. Curiosity and Opportunity are robot geologists that are roaming the surface of the red planet, sending back lots of high-quality data and changing our view of Mars on what seems like a daily basis. NASA are superb access advocates, and every image from these two intrepid machines is posted on their respective websites for us to use; Curiosity's are here.

Five images taken by Curiosity on sol 629 and used for photogrammetrical reconstruction.

I wondered if was possible to generate a 3D mesh from images the rovers had sent back. As it would be useful to record an actual trace I decided to find some suitable images from the hand lens imager. This natty bit of kit is basically the rover's equivalent of the hand lens we all know and love so well. It has a 4cm camera and can resolve features as small as 12.5 micrometers. Sol 629 had what I was looking for, a sequence of images that looked like they might work so I loaded them into Photoscan. The images show a hole drilled by the rover in a martial rock to extract a sample for the onboard sample analysis instruments, plus three smaller marks caused by a laser that is part of the kit that analyses the chemical composition of rock.

In all I used five images from the Sol 629 sequence (3715, 3717, 3719, 3721, 3723). Photoscan was able to produce a high-quality mesh of the hole, the surrounding debris rim and a part of the rock itself. The hole measures 1.63cm across. The illustration above shows the textured mesh, a plain mesh and a mesh coloured according to elevation. The movie below shows a 360 of the mesh.

So what was learnt? Well, we can use as few as five images to generate an accurate mesh. There are some issues around the lip of the hole where the software hasn't recognised the hole itself. The surrounding debris and rock is clearly represented with few artefacts; a perfectly useable mesh.

So we now have a 3D record of one trace on another planet. Exoneoichnology is born, although hardly a new science as humans and their robotic proxies have been leaving marks on other rocky planetary bodies since Luna 2 impacted on the lunar surface in 1959, and Curiosity's wheels are designed to leave the letters 'JPL' in morse code in the Martian dust. We'll have to wait for exoichnology, but hopefully not too long.

What has this got to do with dinosaurs? This exercise is further confirmation that we can use photographic data taken for another purpose to generate robust 3D data for research. Falkingham et al (2014) have successfully done this with the Paluxy River tracks and it is anticipated the technique could be used in the future for this sort of data analysis. Furthermore, if we can't get into the field and our colleagues can then some simple instruction on the picture-taking technique will mean we can have workers gathering 3D data anywhere a palaeontologist (or robot) is present. The possibilities are endless.

*I wondered about the term for the study of traces and came to the conclusion it could be 'astroichnology' or 'exoichnology', as both 'astro' and 'exo' are used as prefixes for 'geology' when studying the rocks of other planets. Exoichnology sounds cooler, so that's what I chose.

Thursday, 12 June 2014

How does a being a part-time PhD researcher actually work in daily life? This is a
question I gave some considerable thought to before I started my doctorate in
January, as I wanted to be sure I could make the commitment to research whilst
working in a job that often means long hours for weeks at a time. Now the
reality is becoming apparent and the past six weeks have gone some way to
answering this question more fully than previously, as the practicalities of keeping research momentum
when the day job gets busy have had to be addressed (see my work here).

As I've mentioned on this blog previously one of my specialities
is creating 3D animations of drug mechanisms of action; these tend to be
commissioned during the middle–later stages of a drug's development
to show the target audience how the drug works at a molecular level. This
involves modelling lots of proteins, cells, viri, bacteria, DNA, RNA etc, often
referring to published data of the structures themselves for accuracy. The
animations are mainly educational in nature (being targeted at consultants and doctors) and are based on some quite
remarkable cutting edge science and I love working on them. They are also
extremely labour intensive and time-consuming.

So recently I've been in full animation production mode and research has
had to be put on the back-burner. Well, almost. Gaps in the production process (which occur for any number of reasons i.e. awaiting assets, team and client review, rendering) for the MOA are little windows of opportunity to keep things moving, even in a
small way. I had photographed most of the vertebral column and some dermal
armour elements of the Polacanthus
specimen I'm working on for processing into 3D data. If a machine is not
rendering a sequence of animation, it can be crunching through these data and
making lovely 3D models of dinosaur bones. Despite being a basic set up, the
results so far have been encouraging; I'm getting good quality, detailed meshes
of the specimen.

My photogrammetry setup. A tad bottom end to be sure, but it's delivering good results.

Periods of reduced work activity also give me time to get on with other small but
essential tasks such as reading and annotating papers, reviews, planning next
steps and keeping up with developments in the field. I use this time to get to
grips with new subjects such as looking at methods of statistical analysis,
bones need measuring and drawing, meetings have to be booked, talks prepared
amongst the myriad of other tasks that need attending to keep the whole process
moving forward.

All this can be done without the slightest disruption to my work
as an artist and graphic designer. Although there are periods where I work long
hours for many consecutive days (running into weeks on large projects) and can't get any research done at all
generally I can take tortoise-like, small steps towards the mountain on a daily
basis.